This R package provides functionality for batch correction methods for mass spectrometry (MS) omics data. This includes Pareto Scaling, Power Scaling, Range Scaling, ComBat, EigenMS, RUV-random, NOMIS, QC-RLSC, WaveICA2.0, SERRF, and TIGER). Additional functions include an imputation function (using expectation maximization algorithms) and a function to filter data for TIGER batch correction. Example data is also provided in the package.
Installation:
devtools::install_github("pmartR/malbacR")Problems with rcppArmadillo and gfortran on mac
malbacR depends on pmartR. There is a problem that causes pmartR to fail compiling cpp code, which has something to do with rcppArmadillo and certain installations of gfortran. See these posts that try to explain the issue: 1 2 3. Two solutions we have found:
- Install gfortran from a recommended source (not homebrew):
- This CRAN-approved resource for build tools on mac lists two versions of gfortran and how to install them.
- On Catalina 10.15.7 I downloaded and installed gfortran 8.2 from the link provided in this blog post
- When using the homebrew gfortran installation, add the line FLIBS = -L`gfortran -print-file-name=libgfortran.dylib | xargs dirname` to ~/.R/Makevars (a plain text file with no extention)
Tutorial:
To get started, see the package documentation and function reference located here.
Data:
Example peptide (both filtered and unfiltered versions) of two metabolite datasets. The first data set (pmart_amide/pmart_amideFilt) is a subset of a dataset originally came from the the R package WaveICA2.0 which can be found here. The second dataset (pmart_mix/pmart_mixFilt) originally came from the R package crmn which can be found here.